\name{readIdatFiles}
 \alias{readIdatFiles}

 \alias{readIdatFiles2}

 
 \title{Reads Idat Files from Infinium II Illumina BeadChips}
 
 \description{
   Reads intensity information for each bead type from
   .idat files of Infinium II genotyping BeadChips}
 
 \usage{
 readIdatFiles(sampleSheet=NULL, arrayNames=NULL, ids=NULL, path="",
               arrayInfoColNames=list(barcode="SentrixBarcode_A",
                                      position="SentrixPosition_A"),
               highDensity=FALSE, sep="_",
               fileExt=list(green="Grn.idat", red="Red.idat"),

               saveDate=FALSE, verbose=FALSE)

 }
 
 \arguments{
   \item{sampleSheet}{\code{data.frame} containing Illumina sample sheet
     information (for required columns, refer to BeadStudio Genotyping
     guide - Appendix A).}
   \item{arrayNames}{character vector containing names of arrays to be
     read in.  If \code{NULL}, all arrays that can be found in the
     specified working directory will be read in.}
   \item{ids}{vector containing ids of probes to be read in.  If
     \code{NULL} all probes found on the first array are read in.}
   \item{path}{character string specifying the location of files to be
     read by the function}
   \item{arrayInfoColNames}{(used when \code{sampleSheet} is specified)
     list containing elements 'barcode' which indicates column names in
     the \code{sampleSheet} which contains the arrayNumber/barcode number
     and 'position' which indicates the strip number.  In older style
     sample sheets, this information is combined (usually in a column
     named 'SentrixPosition') and this should be specified as
     \code{list(barcode=NULL, position="SentrixPosition")}}
   \item{highDensity}{logical (used when \code{sampleSheet} is
     specified). If \code{TRUE}, array extensions '\_A', '\_B' in
     sampleSheet are replaced with 'R01C01', 'R01C02' etc.}
   \item{sep}{character string specifying separator used in .idat file
     names.}
   \item{fileExt}{list containing elements 'Green' and 'Red' which
     specify the .idat file extension for the Cy3 and Cy5 channels.}
   \item{saveDate}{logical.  Should the dates from each .idat be saved
     with sample information?}

   \item{verbose}{logical.  Should processing information be displayed as data is read in?}

 }
 
 \details{

 The summarised Cy3 (G) and Cy5 (R) intensities (on the orginal scale)

 are read in from the .idat files.
 
 Where available, a \code{sampleSheet} data.frame, in the same format
 as used by BeadStudio (columns 'Sample\_ID', 'SentrixBarcode\_A' and
 'SentrixPosition\_A' are required) which keeps track of sample
 information can be specified.
 
 Thanks to Keith Baggerly who provided the code to read in the binary .idat files.
 }
 
 \value{

   NChannelSet with intensity data (\code{R}, \code{G}), and indicator 
   for SNPs with 0 beads (\code{zero}) for each bead type.

 }
 

 \references{
   Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'{e} S, Irizarry RA.
   R/Bioconductor software for Illumina's Infinium whole-genome 
   genotyping BeadChips. Bioinformatics. 2009 Oct 1;25(19):2621-3.
 }
 

 \author{Matt Ritchie}
 
 \examples{
 
 #RG = readIdatFiles()
 
 }
 \keyword{IO}